Change
by kaybet
Summary: Could be called AU, set after the Pond's marriage and after they find out River is their daughter. Plot doesn't follow the plot of the show. The Doctor has been taken and River comes to the Ponds for help. Rated T for a reason.
1. Chapter 1

**This is the first, but also the second and last (wibbly-wobbly timey-whimey) of a bit I'm doing. They are, as well this one, His Nightmare and The Truth. You may read them in whatever order you wish (as soon as they are all up) but I can promise you one thing. I will take you on a mind boggling, oh my god, I got it!, and a holy plot twist, Batman! wild ride. Enjoy. (By the way, thought I should tell you, but this first part is a little gruesome.)**

**Disclaimer: I don't own either Doctor Who nor BBC, otherwise David Tennant would be having a cuppa tea with me right now. Or Matt Smith. Hell, why not them both? If I own them in this imaginary situation imainege what I could do! Mahahahahahaha! I should stop rambling and just give you the story. Oh, and by the way, I don't own the phrase "Holy Plot Twist, Batman!" (Who owns that phrase?)**

_He's been in here for quite a while._

_Days, weeks, maybe even a few months, he couldn't tell. Somewhere during the experiments his internal clock just sorta stopped working. For all he knew, he could have only been here for a few minutes._

_But he knew better than that. The amount of damage that his body has endured already is way too much for just a mere few days. So, he reasoned with himself, it's been longer than that._

_The problem was that he was only awake for maybe, at most, a few hours a day. Whatever they had him on, it was effective. Not many things would work this well against a Time Lord. He would have to congratulate them on how well they had planned this all out when he escape._

_If he escaped, a small part of his mind would whisper back to him. Mentally shaking his head, he couldn't actually move, he reminded himself of the Ponds. They would be here soon._

**Chapter 1**

"Why hello!" Rory said as he opened the opened the door and let River into their home.

"Is that River?" Amy called from the kitchen.

"Hello, mum and dad." River said she hugged Rory and Amy, who was covered in flour, and they sat in the living room.

"How are you, River?" Amy asked.

"I need your help." River said, cutting to the chase.

"What happened?" Rory asked.

"Did something happen to the Doctor?" Amy asked, her face sketched with worried lines.

"Yes, and we need to go and save him."

"Wait, how did you even get here?" Rory asked as they got up.

River said nothing as she opened the door to Amy and Rory's home all the way. At the other end of the street, the TARDIS stood, waiting for her thief.

* * *

_It felt like he had been there forever. He actual forgot where "there" was. He was starting to forget a lot of things lately, like who he was, the roman's name and he was even starting to forget Amy..._

_Not that he was likely to forget her, not completely, who could forget her? The girl who waited... That single thought was the only thing in his head that was likely keeping him sane. Amy Pond..._

_It wouldn't be long... He reasoned with himself, the Ponds would be here soon._

_Everytime they woke him up, it was just for a few minutes at a time. And each time he forgot more and more._

_When would someone becoming for him? It seemed like he has been her forever. Everything was blending together._

* * *

River landed the TARDIS with slightly moist eyes, like she was trying her best not to cry. Amy poked her head out the TARDIS and looked around without stepping out. They landed in front of an unassuming large white building that was only a few stories high. It looked like some type of hospital.

"Is this where he is?" Rory asked River. He noticed that she was on the verge of tears and put a comforting arm around here.

"Yes. Here, take the psychic paper and the sonic," River said as she gave Amy and Rory the items. "You two go through the front and pretend you work here, I'll go through the back and meet you here, in the servanlace office." River explained as she showed them the schematics of the building, showing them where to go. "Then, we'll find him."

Amy and Rory, following River's plans, walked together down the stark white halls, labs coats on. Getting in had been relatively easy, all they had to do was to show the psychic paper to  
the oaf security guard and they were allowed in. Even getting the lab coats and ID cards were easy, they were in a spare closet, along with two people who were fast asleep and, well, mostly naked.

Finding the security office had been just as easy, and this surprised Amy a bit and made her uneasy. Nothing was ever this easy, and something as big as this should have been a lot harder, not as simple as it was going so far.

As Rory used the sonic screwdriver to open the door Amy stood guard, making sure nobody would stop them. And nobody did. This flared her paranoia even more as several people walked by and didn't do anything while it took Rory several minutes to figure out how to unlock the door.

* * *

_They, whoever they were, by then he had forgotten about it, started to take him off whatever they had pumped through his veins._

_It hurt. Whatever they were doing, it hurt. Flesh that was deadened by the drugs slowly thawed back to life painfully. But he quessed that coming back from the dead was bound to hurt, and there was really nothing to do about it, besides putting him back under._

_Not that they would show an act of kindness, whatever they are._

_The drugs must have worn off faster then they have thought, because when he was finally able to open his eyes, a blurred creature, that was previously staring intently at him, pulled back from sudden surpize and let out an inadoiuble ohh._

_This was the perfect time for an escape. He used to be so good at escapes, he thought as he tested out his muscles, some of them, exspecial in his limbs, were a bit unresponsive, but they would have to do. Somewhere in his mind, small voice whispered._

_The Ponds weren't coming for him._

_This idea, fresh in his mind, brought tears to his eyes, blurring everything even more. Whispers, from the outside, not in his head, filled his ear canals. He couldn't understand any of them, but could defently tell what laungage it was._

_English. He was surrounded by humans._

* * *

When Rory finally managed to get the door to the security office open, River had already gotten there and was sitting at the desk, waiting for the Ponds. Amy was the first to get in and Rory closed the door gently behind him and locked it.

"So, where's he at?" Amy asked impatiently as she peered at the monitor screen over River's shoulders. The screen switched cameras and showed various hallways and rooms, but no Doctor.

"Give me a second." River said as she typed, her fingers moving gracefully over the keyboard, but to no avail. A pop-up appeared onscreen and informed the trio that their access was denied.

"Access denied?" Rory asked. "Why?"

"Well, it certainly means we looking in the right place." River responded and she continued typing.

* * *

_"I think he's waking up..." A voice said cautiously. Female, maybe around her early thirties. The first clear voice he's heard in a long time._

_He snapped his eyes opened and pulled away from from the people that were surronding him. The humans. They were weak and he pulled away from them easily, although his newfound strength was quickly starting to diminish, and he pushed out the first door he found, not bothering even to take in his surroundings, and he ran._

* * *

"Ha!" River exclaimed as she bypassed the security of the building's mainframe and the annoying access denied disappeared and information filled its place on the screen. Information about Time Lord biology.

"Wait, what does it mean? River?" Amy asked as the information continued to pour on screen and River's small smile of triumph disappeared. She click on something and pictures began to fill the screen.

"Oh my god." Amy whispered under her breath, the words losing strength on her tongue. The pictures were all of the Doctor, being experimented on. Terrible gruesome pictures, of bruises, small cuts, the Doctor's insides...

"What have they been doing to him?" Rory asked to no one in particular as pictures continued to fill the screen. All of them were as equally horrible and made him sick to his stomach, and he had seen some pretty gruesome things, being a nurse and traveling with the Doctor. But nothing like this.

Suddenly an alarm rang through the building and a man was shouting on the PA system. _The Doctor has escaped. I repeated: The Doctor has escaped. The building is now in lockdown mode._

* * *

_It felt he had run forever down those never ending, stark white blank hallways. As he rounded another corner, his leg muscles threatening to give out from under him, he ran straight into a group of men in body armor and each carrying firearms, pointing at him._

* * *

As Rory and Amy rushed to the door, River kept at the computer and switched over to the security cameras.

"The door! It's locked!" Rory yelled as he frantically tried to pull it open.

"Use the screwdriver, stupid!" Amy yelled back. Rory pulled the device quickly from his pocket and in his panic, he dropped it and it rolled under the narrow slit under the door.

"No, no, no, NO!" Amy yelled as she scrambled for the sonic screwdriver, but it was too late, it was out of her reach.

"Mum, Dad, I think you need to you need to see this." River said as Amy got to her feet and faced Rory, her face expressing defeat.

"What, River? What is it?" Rory asked as he turned away from his wife and looked at River. She was pointing at the screen, where the Doctor was front and center, sprinting down the hallway for his life.

* * *

_He raised his arms in defense, and something was about to slip out from his mouth, probably a lie to somehow get him out of this, but before the words even slipped out of his lips, they fired and he sank to his knees, dying._

_A familar vibrating, almost a buzzing feeling, coursed through his bones and his skin began glow, a golden light floated from his skin and covered everywhere._

_All he could see was light, a golden light._

_Then there was nothing._

**See that little bow below this? It's a handy-dandy place where you type in your review and I get to see it! Amazing technology, anitt?**


	2. Chapter 2

**Chapter 2**

The three Ponds starred in mute shock as they witnessed, live, as the Doctor was blocked by men with guns. Amy started to cry as she watched the scene unfold in front of her eyes. As if the cameras played back in slow motion, the men started to fire at the Doctor and she wept as every bullet hit the Doctor.

"No." She mouthed silently as the Doctor fell to the floor. Golden light began to float off of his hands and soon covered him completely. River, in front of her, began to cry as well and so had Rory.

The camera that was focused on the doctor went out as the light continued, leaving them with a screen that was just filled with static snow. Amy grabbed Rory in a tight hug and sobbed into his chest while he hugged her and River hugged both of them.

They stood there for easily twenty and cried into Rory's shoulders. Amy was sobbing, her Raggedy Man was gone, and she wasn't able to save him.

_The lockdown is now over, I repeat: The lockdown is now over._ The man came over the PA system and announced to the building. The door that they tried so desperately to open to get to the Doctor clicked and it unlocked. Rory let go of his wife and daughter and tested the door out. It opened with ease and he picked up the sonic screwdriver where it was lying a few inches from the door. Rory closed the door again and looked at the girls.

"We're going to find him. No matter what he looks like now, no matter where he is, we will find him." Rory said adamantly. River nodded and returned to the computer and started typing furiously. Rory moved over to where Amy was still standing and sobbing.

"It's okay... shhh." Rory said as she continued to sob in his chest. She eventually stopped and looked up at Rory. "Everything will be okay, I promise."

"Got him!" River said suddenly from the desk. Rory and Amy both rushed over and took separate sides and peered at the screen. It was a map and there was a red dot far off the beaten path. "There he is!" River cried.

"Right, lets go." Rory said and they raced out the door towards the center of the hell where the Doctor had been held for a month.

Like getting in, getting there had been suspiciously easy. Nobody noticed them until they got to the section of the building where the Doctor was being held.

There were two security guards standing outside of the door that led into the section. River approached casually and held up the psychic paper.

"You know, we've been trained against the Doctor's little tricks, gorgeous." One, a large white male with brown hair, said casually, as if this was a normal conversation. "You one of his companions trying bust him out?"

"No," River replied normally, keeping up with the normal conversation, "I'm his wife." She said and punched the guard squarely in the nose. Rory popped up from behind her and took out the other guard. Amy held up the sonic and unlocked the doors, allowing the other two to get in.

"This way." River whispered to the two Ponds as she led them down a labyrinth of halls. They rounded a corner and saw that in the middle that there was a sanitation team working hard to clean up blood that was all over the hallway floors and walls.

Rory felt Amy behind him take in a sharp breath as she tried not to cry at the scene. "Come on," he whispered to River, who was in front of him. He could tell that she was struggling not to cry as well. "Let's find a different way around."

River nodded curtly and led them down a different hall, away from the gruesome scene of the Doctor's death and regeneration.

They continued down the white halls trying to find a way to the Doctor. Rory could tell from behind him that Amy was struggling not to break down sobbing at the loss of her Raggedy Man. All Rory wanted to do was to turn around and comfort his wife, but he couldn't. Not yet.

Finally they managed to bypass the cleaning team and made it back on the path to the Doctor. The trio didn't encounter many people, they were all rushing around them, clearly too busy to notice them. Soon, a little too soon, Rory thought, they reached the door where that led to where the Doctor was being held.

Understandable, it was crawling with guards who were a bit skittish after the Doctor's attempted to escape.

River gathered the Ponds around her in a tight little group. "We need to find a way around them," She whispered as she looked around. "Everybody here has probably been trained against the psychic paper."

Rory looked around and knew River was right. There was no way they would be able to get past all these guards, not with the paper and not alone. He saw a supplies cardboard on the right. "Okay, listen." Rory said to the girls and he told them his plan.

They waited in the supplies cardboard for a few hours until everything quieted down. It was nighttime and someone waxing the floor just passed when Rory opened the door it was empty. "The guards must be on break." He whispered to the others and let them out.

Nobody spoke as River led the two Ponds down the hallway to the door that the Doctor was behind. There was a scanner and River took the sonic screwdriver from Rory's hands and quickly opened it.

"We need to be quick." River said to the Rory and Amy before she opened the door complete and they slipped in like thieves in the night.

The door led to another long hallway that had windows that showed large rooms with a metal table in the middle with straps. As the trio sped walked quietly down the hall, the noticed that all of the rooms were empty. But, at the very end of the hallway, there was a single room that wasn't empty. On the table, which was currently upright, there was a teenage girl that was bone thin. Her chin was touching her chest and bobbing slightly up and down with her slow breathing. She had shoulder length dark brown hair.

"Who is that?" Amy asked Rory quietly and he shook his head.

The girl, who was quietly sleep, it seemed, suddenly lifted her head up and opened her mouth. A golden glittery-like energy slipped out from between her lips and dissipated in the air. Amy looked at Rory with a shocked look upon her face.

The girl strapped to the cold metal table was_ the Doctor._

**Remember about that box that I told you about last chapter? It is truly spectacular. Try it out! And remember; the more I get helpful comments and reviews, the better I write.**


	3. Chapter 3

**Chapter Three**

Amy and Rory stared in shock at the girl strapped to the table. "But... how..." Rory stammered, unable to form a coherent sentence.

"But, that's her..." Amy said, seeming to read Rory thoughts and making them make sense.

"Come on!" River whispered loudly and pulled the Ponds along the hallway and away from the observational window to the nearby door. She turned on the sonic and the door unlocked with a satisfying click.

River rushed inside the small hallway and swung opened the door that separated her from the Doctor and the Ponds followed her. River rushed over to the girl and lowered the table until it was parallel with the ground and started undoing the straps.

"Help me!" River quietly begged Rory and Amy, who were looking around the room at the surgical instruments and hospital equipment that laid scattered about, some of them bloody. Rory snapped his head up at his daughter and rushed over to the table and began to help undo the many straps.

As he undid the straps, Rory noticed that there were deep purple bruises and small cuts from where the straps held her in, as if she struggled against them. As River began to take out the numerous IV needles from the Doctor, her eyes fluttered open.

"Hey there." Rory said quietly as he cupped his hands around the new Doctor's face and looked into her eyes. Before they closed again, Rory noticed that they were a deep blue, a very similar color to the TARDIS.

"She passed out." Rory said to River as he let go of the Doctor's small face. Her face was tiny, especially when he mentally compared it to Amy's Raggedy Man's face. She was small overall.

"Let's get her out here." River whispered to Rory as soon as she was done removing everything that was attached to the girl. Rory nodded and picked her up, surprised at how much she weighed. She couldn't have weighed more than ninety pounds at most. She was just so small.

"Right. Amy, let's go." Rory said as he adjusted the fragile form in his arms.

"Shhh, there's a guard right there." Rory whispered to the girls as they rounded a corner. Rory pushed them back as best as he could with the still form of the Doctor in his arms. She hasn't moved or even made a sound since they freed her from the metal table. Rory wasn't even sure she was breathing.

They waited until the guard made his way past and they continued down the labyrinth of darkened hallways, River leading, Rory in the middle with the Doctor and Amy held up the rear. All was quiet, too quiet for anybody's liking. There ought to be a lot more security around here, Rory thought as he again readjusted the Doctor. Even though she barely weighed anything, he arms were getting sore from the weight he was holding her.

As they passed the door that led into the normal section of the building, an alarm started to sound, an angry screeching that was so loud that Rory dropped to one knee and dipped his head to avoid the pain that rang throughout his ear canal. Painfully, he looked to his side to see his wife. Amy was holding her head with her hands trying to block out the nosie. River doing the same thing, but instead of kneeling she was still somewhat standing and leaning against the wall, slowly sliding down.

But as soon as the alarm started, it stopped. The three looked around and saw the hallway was just as empty as it had been earlier. But through ringing ears they could hear the heavy footsteps of security guards running down the halls towards their location.

"River, Amy, we need to get out of here, now." Rory said, taking charge of the situation. He shifted the Doctor in his arms long enough to help Amy up. She took his hand gladly and pulled herself up.

"Right," Amy said as she brushed herself off, still whispering, "let's go this way." She pointed to the opposite way as the sound of the guards' footsteps. Rory nodded to his wife and followed her lead.

The trio ran on, Rory tried to run carefully so he wouldn't harm the Doctor anymore than she was already injured. But, even as fast as they ran, the guards still caught up with them. As they rounded a corner they ran into five security guards, all with semi-automatics in there hands, pointing right at the Ponds and the Doctor.

"Put the Doctor down." A large african american from the middle of the group spoke. He had a deep voice, and that scared Rory even more.

"Or what?" Amy asked as she bravely stepped in between the guards and the Doctor.

"Or we will kill you all." Another guard answered calmly.

"We are not going anywhere." Rory said, both to Amy and the guards. "Why did you take the Doctor?"

"Why else? He's an alien and very useful." Another guard answered with a slight chuckle. Rory felt sick to his stomach when he said that, imagining the things they did to the poor girl in his arms.

"Gents, click off your safeties." The guard in the middle said and the others complied.

"Oh, no." Rory whispered as they prepared their weapons to fire.

Without warning, the still form of the Doctor in Rory's arms sprung to life and she grabbed the sonic screwdriver from River's hand and pointed at the guards. The green light at the end switched on and the sonic came to life. JUst as the guards began to fire, all their weapons simultaneously misfired and jammed, rendering them useless.

Just as suddenly as the Doctor had awoken and sprung to action, she passed out in Rory's arms and the screwdriver rolled from her fingers and onto the floor, still on when River bent over to pick it up.

"Let's go." River said to the Ponds as she switched the sonic off and the trio ran past the guards, who were frantically trying to fix their weapons.

"After them!" A guard yelled as the River, Rory and Amy rounded a corner and saw the exit at the end of the hall. As the ran, River opened the door with the sonic and they shot out of the door and ran as fast as their legs could carry them to the TARDIS.

The TARDIS opened her doors in advanced as the Ponds reached her. The guards that were following them were shut out when the TARDIS closed her doors in their faces and disappeared in front of their eyes.

"How is she?" River asked as she put the TARDIS into the time vortex. It was humming a quiet lullaby, instead of the loud wheezing and clanking noises that it made when the Doctor was driving. River guessed that the old girl didn't want to wake her poor, injured thief.

"Pulse is steady..." Rory said as he examined the Doctor, "I think." He added. "And he breathing's fine. Are we out of danger?" He asked River as he continued to search the girl for obvious injures.

"Yes, we are." River said and came over to where Rory and Amy sat next to the Doctor who laid on the floor near the door. "We should take her to the med bay." River said to Rory and he gently picked the Doctor up.

"Where's the med bay?" Rory asked.

"No idea, but I bet it's somewhere close." River responded and she led them down the warm halls of the TARDIS. "Here it is." She said a little way in and opened the door. Inside was a large room with a few beds and medical equipment carelessly scattered about.

"What do we do?" Rory asked as he set the Doctor down as gently as he could manage on to the first bed in the room. River pulled over a monitor that was attached to the ceiling to Rory's view and started pressing buttons. None of it was in English until River pressed something and it beeped and convert to English so that Rory could read it.

"Scanning her right now." River mumbled as she continued to press buttons. The Doctor's form showed up on screen and Rory could see that she was mostly fine, just a few bruises and cuts. Nothing broken and no internal damage.

"I think's she's out of danger..." Rory said to River and Amy as he looked at the screen for less obvious damage. "But we should probably start a drip, she looks malnourished and a bit dehydrated." Rory said as the nurse instincts inside woke up and he looked for the proper bag.

"Mum, I think you should go lie down." River said to Amy as soon as Rory started to search the great expansive med bay. Amy looked up at her and River saw how uneasy and pale she was.

"Yeah, that's probably a good idea." Amy admitted and left the med bay. She felt ill about the whole situation. First, her Raggedy Man was dead, he was killed and there was nothing she was able to do about it, and secondly, that her Doctor, _her Doctor_ was gone and has turned into... that... _monster._


End file.
